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Structural analysis and insights into glycon specificity of the rice GH1 Os7BGlu26 beta-D-mannosidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RGL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.25 288 0.8M K,Na tartrate, 0.1M Na HEPES, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.89 57.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.084 α = 90 b = 71.685 β = 90 c = 136.675 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 315 2009-08-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.21 25.49 99.6 34370 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 99.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2RGL 2.21 25.49 32558 1733 99.59 0.17841 0.17626 0.1774 0.21921 0.2204 RANDOM 23.883
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.17 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.177 r_dihedral_angle_4_deg 19.22 r_dihedral_angle_3_deg 14.453 r_dihedral_angle_1_deg 5.719 r_scangle_it 2.402 r_scbond_it 1.709 r_angle_refined_deg 1.155 r_mcangle_it 0.957 r_mcbond_it 0.858 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.177 r_dihedral_angle_4_deg 19.22 r_dihedral_angle_3_deg 14.453 r_dihedral_angle_1_deg 5.719 r_scangle_it 2.402 r_scbond_it 1.709 r_angle_refined_deg 1.155 r_mcangle_it 0.957 r_mcbond_it 0.858 r_nbtor_refined 0.307 r_symmetry_hbond_refined 0.202 r_nbd_refined 0.188 r_symmetry_vdw_refined 0.163 r_xyhbond_nbd_refined 0.129 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3934 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms 51
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling